Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Robustness towards alignment errors and INDELs for methods in HY (Read 1005 times)
Jae
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 9
Robustness towards alignment errors and INDELs for methods in HY
Aug 28th, 2012 at 6:25am
 
Hello Developers of HYPHY

I had a general question wondering if methods such as Branchsite REL or MEME have been examined for its performance under different aligner programs?

I understand PAML and SLR have looked into this issue and I was wondering if the developers of HYPHY have similarly looked into this?

And I apologize if this has been mentioned somewhere else.

Thank you very much

Sincerely

Jae
Back to top
 
 
IP Logged
 
konrad
Junior Member
**
Offline


I love YaBB 1G - SP1!

Posts: 53
Re: Robustness towards alignment errors and INDELs for methods in HY
Reply #1 - Aug 28th, 2012 at 2:13pm
 
Dear Jae,

Alignment quality is definitely important and can have a strong effect on any of these evolutionary analysis. To my knowledge, the effect has not been analyzed extensively (either by us or by the developers of PAML and SLR) beyond pointing out that it is there and that evolutionary analyses on poor alignments cannot be trusted.

The bottom line is to always inspect alignments manually and be aware that any alignment errors may cause incorrect inference of phylogeny and/or selection.

Hope this helps,
Konrad
Back to top
 
WWW WWW  
IP Logged